NFR are generally not considered part of the set for collection purposes with regard at least to the Charms here on VGS. Most places will tell you, I believe, that only those games offered at retail "count" for a set, while anyone who goes beyond that is simply going above and beyond.
As far as me checking your games for charm purposes, frankly I personally am rather lazy in this regard - I generally will take you at your word for that the photos you present as being a "complete set" are indeed the whole set. I don't like, magnifying glass to the screen and make sure you have every single title. For specific sets I might go "no way this dude has Super Rare Game X" and double check that, but that's about as far as I go.